Some of it for me, is in his switching. Now, I can hear it. Back in the day, his tones blended seamlessly, he went from warm round clean to high gain and you didn't notice the change until well after it happened. CK's lights were the same, his fades and blends were far superior back then to the button pressing switching now.
Analog days. They are gone, and while Trey (and CK) has way more in his arsenal now, it doesn't have that same wow factor. Less is more? Or maybe when you have limits to what you work with, creativity kicks in more. (Original Trilogy vs. Prequels).
Damn progress (0).

I'm skipping Walnut Creek in favor of a show in LA two years ago. I am pretty sure this one was webcast and remember watching it with many of you all. 7/22/16
https://phish.in/2016-07-22/halfway-to-the-moon
I noticed an extremely extremely trivial thing going on at the time. If you listen to roughly around 40 seconds in, take a listen to Fish's beat. Instead of the relatively simple way he normally plays the song, he uses his ghost note pattern that is very prominent throughout lots of the band's early works (David Bowie, parts of YEM, Hood, etc). It basically consists of him playing 16th notes on his snare with an accent on 2 and 4. It is actually one of the elements of Fish's drumming that got me into his playing and into the band altogether way back when!
Now normally, this wouldn't matter. But this subtle change leads to what I consider a splendid version of Halfway. That extra umph makes a huge difference in the pace of the song and makes it go from mid-set snooze-fest to up-beat mood-lifter. Unfortunately, this seems to have been a one-time thing - I hadn't heard it before and haven't heard it since. Ultimately it was probably one of those things that Fish just tried and forgot all about 40 odd times they've played the tune. Maybe I'll bring it up if I ever chat with him again.

ive been saying this about troy's playing since 12/31/2002. his 1.0 tone is still the greatest, most warming, encompassing tone ive ever heard from any guitar player, ever. its what made those days so special.